Estimating enrichment of repetitive elements from high-throughput sequence data

We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for...

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Detalles Bibliográficos
Autores principales: Day, Daniel S, Luquette, Lovelace J, Park, Peter J, Kharchenko, Peter V
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911117/
https://www.ncbi.nlm.nih.gov/pubmed/20584328
http://dx.doi.org/10.1186/gb-2010-11-6-r69
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author Day, Daniel S
Luquette, Lovelace J
Park, Peter J
Kharchenko, Peter V
author_facet Day, Daniel S
Luquette, Lovelace J
Park, Peter J
Kharchenko, Peter V
author_sort Day, Daniel S
collection PubMed
description We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3/H3K9me3 differences among the endogenous retroviral element classes.
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spelling pubmed-29111172010-07-28 Estimating enrichment of repetitive elements from high-throughput sequence data Day, Daniel S Luquette, Lovelace J Park, Peter J Kharchenko, Peter V Genome Biol Method We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3/H3K9me3 differences among the endogenous retroviral element classes. BioMed Central 2010 2010-06-28 /pmc/articles/PMC2911117/ /pubmed/20584328 http://dx.doi.org/10.1186/gb-2010-11-6-r69 Text en Copyright ©2010 Day et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Day, Daniel S
Luquette, Lovelace J
Park, Peter J
Kharchenko, Peter V
Estimating enrichment of repetitive elements from high-throughput sequence data
title Estimating enrichment of repetitive elements from high-throughput sequence data
title_full Estimating enrichment of repetitive elements from high-throughput sequence data
title_fullStr Estimating enrichment of repetitive elements from high-throughput sequence data
title_full_unstemmed Estimating enrichment of repetitive elements from high-throughput sequence data
title_short Estimating enrichment of repetitive elements from high-throughput sequence data
title_sort estimating enrichment of repetitive elements from high-throughput sequence data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911117/
https://www.ncbi.nlm.nih.gov/pubmed/20584328
http://dx.doi.org/10.1186/gb-2010-11-6-r69
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